Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nfil3

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
E4BP4 TG - E4BP4
strain
C57BL/6
age
8 week old
Sex
male
genotype/variation
liver-specific E4BP4 transgenic
tissue
liver
chip antibody
E4BP4 (sc-28203, Santa Cruz Biotechnology)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After cervical dislocation, mouse liver was perfused with a buffer containing Hanks' balanced salt solution, and cross-inked for 30 minutes with 2mM DSG and for 10 minutes with 1% formaldehyde by perfusion, followed by frozen at -80C. Then, Liver was homogenated by gentleMACS Dissociators. Nuclei were isolated in buffer containing 1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.0, and protease inhibitors and sonicated using a Diagenode Bioruptor to shear chromatin to 200-1000bp fragments. Protein-DNA complexes were incubated with antibodies against two kinds of E4BP4 (sc-28203, Santa Cruz Biotechnology)and immunoprecipitated with IgG paramagnetic beads (Invitrogen). Eluted chromatin was isolated using MinElute PCR purification columns (Qiagen). Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions. Library concentrations were assessed by both a Bioanalyzer (Agilent) and NEBNext Library Quant Kit for Illumina (New England Biolabs).

Sequencing Platform

instrument_model
NextSeq 550

mm10

Number of total reads
31448578
Reads aligned (%)
94.4
Duplicates removed (%)
21.8
Number of peaks
335 (qval < 1E-05)

mm9

Number of total reads
31448578
Reads aligned (%)
94.2
Duplicates removed (%)
21.9
Number of peaks
349 (qval < 1E-05)

Base call quality data from DBCLS SRA